PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Vradi03g03410.1

Organism

Vigna radiata

Taxonomic ID

157791

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna

Family

C2H2

Protein Properties

Length: 522aa MW: 56960.5 Da PI: 9.1435

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Vradi03g03410.1	genome	SNU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.1	3.2e-05	87	109	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Vradi03g03410.1 87 FICEICNKGFQRDQNLQLHRRGH 109 89*******************88 PP
2	zf-C2H2	13.9	0.00016	163	185	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Vradi03g03410.1 163 WKCEKCSKKYAVQSDWKAHTKTC 185 58*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.4E-5	86	109	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.2E-6	86	109	No hit	No description
Pfam	PF12171	6.3E-5	87	109	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.022	87	109	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.845	87	109	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	89	109	IPR007087	Zinc finger, C2H2
SMART	SM00355	130	128	158	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.7E-5	151	184	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.2E-6	158	183	No hit	No description
SMART	SM00355	130	163	183	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010075	Biological Process	regulation of meristem growth
GO:0045604	Biological Process	regulation of epidermal cell differentiation
GO:0048364	Biological Process	root development
GO:0051302	Biological Process	regulation of cell division
GO:0003676	Molecular Function	nucleic acid binding
GO:0042803	Molecular Function	protein homodimerization activity
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 522 aa Download sequence Send to blast
MMDGAAGTHG SVFLSPHNDY AVTEYHGREP FSLSSTLPGL PNEQNTNPNP NHPPPPTKKK 60 RNLPGTPDPD AEVIALSPKT LMATNRFICE ICNKGFQRDQ NLQLHRRGHN LPWKLRQRSN 120 KEVRKKVYIC PEKTCVHHHA SRALGDLTGI KKHYSRKHGE KKWKCEKCSK KYAVQSDWKA 180 HTKTCGTREY KCDCGTLFSR KDSFITHRAF CDALAEESSR LSSVTTSSLN FKSEDASVMN 240 TQAGLSSCEL ITGQGMQSVP HFGPHGFRLM GMGADQQRPN LSLWLNQGHH INNPLDVPSS 300 SSSGLPEVVQ MAQANNALID SSSVFSNFRM PASNSKGEGG ASDLATIYSE SQNKNSISAS 360 PMSATALLQK AAQMGSTRST NPSIFSGSFG VMSSSSTQST SLNNRNANQT GDQLNQVFHN 420 MNRQENFNGT SSSATMLGSS SNFSSLTHPS NSFDQFLMQN NVEPTQINLH PGSNTVEHNL 480 TRDFLGMNRN GGGHPFLPEE LAKFASLGSS MGLNQFIAGH Q*

Sequence ? help Back to Top

Protein Sequence Length: 522 aa Download sequence Send to blast

MMDGAAGTHG SVFLSPHNDY AVTEYHGREP FSLSSTLPGL PNEQNTNPNP NHPPPPTKKK  60
RNLPGTPDPD AEVIALSPKT LMATNRFICE ICNKGFQRDQ NLQLHRRGHN LPWKLRQRSN  120
KEVRKKVYIC PEKTCVHHHA SRALGDLTGI KKHYSRKHGE KKWKCEKCSK KYAVQSDWKA  180
HTKTCGTREY KCDCGTLFSR KDSFITHRAF CDALAEESSR LSSVTTSSLN FKSEDASVMN  240
TQAGLSSCEL ITGQGMQSVP HFGPHGFRLM GMGADQQRPN LSLWLNQGHH INNPLDVPSS  300
SSSGLPEVVQ MAQANNALID SSSVFSNFRM PASNSKGEGG ASDLATIYSE SQNKNSISAS  360
PMSATALLQK AAQMGSTRST NPSIFSGSFG VMSSSSTQST SLNNRNANQT GDQLNQVFHN  420
MNRQENFNGT SSSATMLGSS SNFSSLTHPS NSFDQFLMQN NVEPTQINLH PGSNTVEHNL  480
TRDFLGMNRN GGGHPFLPEE LAKFASLGSS MGLNQFIAGH Q*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	4e-38	159	225	3	69	Zinc finger protein JACKDAW
5b3h_F	4e-38	159	225	3	69	Zinc finger protein JACKDAW
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	113	125	KLRQRSNKEVRKK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:20356954, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440, ECO:0000269\|PubMed:28211915}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00485	DAP	Transfer from AT5G03150	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Vradi03g03410.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by SCR and SHR. {ECO:0000269\|PubMed:21935722}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AP015037	0.0	AP015037.1 Vigna angularis var. angularis DNA, chromosome 4, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_014494930.1	0.0	zinc finger protein JACKDAW isoform X1
Swissprot	Q700D2	1e-132	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A1S3TMD7	0.0	A0A1S3TMD7_VIGRR; zinc finger protein JACKDAW isoform X1
STRING	XP_007162739.1	0.0	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF181	34	275

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03150.1	1e-109	C2H2-like zinc finger protein

Publications ? help Back to Top
Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938]